Encog 2.1 for DotNet seems to work just fine with Mono. I downloaded a VMWare virtual machine from the Mono project to test it. You can see a screen shot of the OCR example program running under Mono and the SUSE Linux operating system. I did not need to recompile anything. I just downloaded the Encog C# examples, navigated to the OCR application folder and entered:
mono OCR.exe